The H7 subtype of avian influenza (AI) has the capability to evolve into a highly pathogenic AI (HPAI) virus. In this study, we have characterized the hemagglutinin (HA) genes of three avian H7N7 influenza A viruses isolated from healthy migratory mallards in Northern Europe in three different years to study the natural variation of these viruses in the natural reservoir. Phylogenetic analysis demonstrated that the H7 HA genes were all closely related to recent H7 isolates responsible for influenza outbreaks in poultry in Europe. The A/mallard/Sweden/S90735/2003 isolate clustered together with the HA gene of A/mallard/Netherlands/12/00/H7N3 (AY338460), which has been shown to be closely related to the H7N7 responsible for HPAI outbreaks in the Netherlands and Germany in 2003. In contrast, the HA gene of the two mallard strains A/mallard/Sweden/S90597/2005 and A/mallard/Sweden/100993/2008 were more related to the chicken strain isolated in domestic poultry in England in 2006, A/Ch/England/4054/2006/H7N3 (EF467826), and 2008, A/Ch/England/2008/H7N7 (214011964). Analysis of the deduced HA amino acid sequence shows two different HA cleavage sites in these isolates. Although these HA cleavage sites are consistent with a low pathogenicity AI, the cleavage sites appear to posses an increasing numbers of basic amino acids over time (PEIPKGRGLF in 2003 and 2005 and PEIPKKRGLF in 2008). The conclusion from this study is that H7 subtypes isolated from healthy mallards are closely related to the H7 subtypes that have caused recent influenza outbreaks in poultry in Europe.